The answer is emphatically - no, the correct integral should not involve absolute values.
To fully understand what's going on, it should suffice to examine the simpler situation
Integrate[1/z, z]
(*Out: Log[z] *)
Presumably, the expected answer is, as we learn in calculus 1:
$$\int \frac{1}{z} \, dz = \ln\left|z\right|+c.$$
As Junho points out in his answer, however, Mathematica generally assumes that everything is complex and, in the complex context, the above anti-differentiation formula is simply not correct. In fact, $F(z)=\ln\left|z\right|$ is not even differentiable so it certainly can't be the anti-derivative of $1/z$ or anything else. A quick way to see this with Mathematica is to compute:
D[Log[Abs[z]], z]
(*Out: Abs'[z]/Abs[z] *)
Well, that's not 1/z. In fact, it's complete nonsense, as the absolute value function is nowhere differentiable as a complex function.
The most elementary way to see what's going on mathematically is via the Cauchy-Riemann equations, i.e. if we separate a complex function into its real and imaginary parts,
$$f(z)=f(x+iy)=u(x,y)+i\,v(x,y),$$
we have
$$u_x = v_y \; \text{ and } \; u_y=-v_x.$$
Examining $f(z)=1/z$, for example,
ComplexExpand[1/(x + I*y)]
(*Out: x/(x^2 + y^2) - (I y)/(x^2 + y^2) *)
and
Simplify[D[x/(x^2 + y^2), x] == D[-y/(x^2 + y^2), y]]
(*Out: True *)
Now, suppose we apply this to the purported anti-derivative $\ln\left|z\right|$. Since this function is purely real valued, it's expansion into real and imaginary parts is
$$\ln\left|z\right| = \ln\left|x+i\,y\right| = u(x,y)+i\,v(x,y) = \ln\left(\sqrt{x^2+y^2}\right) + 0\,i.$$
Thus
$$u(x,y) = \ln\left(\sqrt{x^2+y^2}\right) \; \text{ and } \; v(x,y) = 0.$$
But, then, the Cauchy-Riemann equations are not satisfied!
Now, let's examine Mathematica's choice. Again:
Integrate[1/z, z]
(*Out: Log[z] *)
where Log is base E. It appears to work out, as far as the derivative is concerned:
D[Log[z], z]
(*Out: 1/z *)
Let's see if Log[z] satisfies the Cauchy-Riemann equations. We'll start with a ComplexExpand:
antiDerivative = ComplexExpand[Log[x + I*y]]
(*Out: I*Arg[x + I*y] + Log[x^2 + y^2]/2 *)
Well, the Arg function makes things a bit tricky here since, like Abs it's not differentiable. We can replace Arg[x+I*y] with ArcTan[y/x], though to obtain an analytic expression. Then
Simplify[D[Log[x^2 + y^2]/2, x] == D[ArcTan[y/x], y]]
(*Out: True *)